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<a href="#pub-types">Public Types</a> &#124;
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<p><code>#include &lt;<a class="el" href="_argument_handler_8hpp_source.html">ArgumentHandler.hpp</a>&gt;</code></p>
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<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-types"></a>
Public Types</h2></td></tr>
<tr class="memitem:ae693a55bec1ed6005f0976a40a7f854a"><td class="memItemLeft" align="right" valign="top">enum &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="class_argument_handler.html#ae693a55bec1ed6005f0976a40a7f854a">InputType</a> { <a class="el" href="class_argument_handler.html#ae693a55bec1ed6005f0976a40a7f854aafe3d262ec86ee31ed3d27ef42b1f235a">alignment</a>, 
<a class="el" href="class_argument_handler.html#ae693a55bec1ed6005f0976a40a7f854aa9d20bc1085ccd1932c0ffd1d97a10dc6">distance</a>
 }</td></tr>
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<tr class="memitem:ae260b096d1b4cb57e0539b8d37ca1ce6"><td class="memItemLeft" align="right" valign="top">enum &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="class_argument_handler.html#ae260b096d1b4cb57e0539b8d37ca1ce6">OutputType</a> { <a class="el" href="class_argument_handler.html#ae260b096d1b4cb57e0539b8d37ca1ce6a1af730d3ffbdc6354d6bda2549356cef">dist</a>, 
<a class="el" href="class_argument_handler.html#ae260b096d1b4cb57e0539b8d37ca1ce6ab25e481414af792cbeffe6f6e2f06301">tree</a>
 }</td></tr>
<tr class="memdesc:ae260b096d1b4cb57e0539b8d37ca1ce6"><td class="mdescLeft">&#160;</td><td class="mdescRight">The output type can be either a distance matrix or a tree.  <a href="class_argument_handler.html#ae260b096d1b4cb57e0539b8d37ca1ce6">More...</a><br /></td></tr>
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<tr class="memitem:ac2a6552abc7c6449b625791aefdf6d87"><td class="memItemLeft" align="right" valign="top">enum &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="class_argument_handler.html#ac2a6552abc7c6449b625791aefdf6d87">AlphabetType</a> { <a class="el" href="class_argument_handler.html#ac2a6552abc7c6449b625791aefdf6d87af8d1253b6d8eecce0eea5eff86ddc63e">dna</a>, 
<a class="el" href="class_argument_handler.html#ac2a6552abc7c6449b625791aefdf6d87abf0a7e58c2a951cb200e05ceed789d48">amino</a>, 
<a class="el" href="class_argument_handler.html#ac2a6552abc7c6449b625791aefdf6d87a340fde3e9bbd6b4f6450c7e10baa63a4">null</a>
 }</td></tr>
<tr class="memdesc:ac2a6552abc7c6449b625791aefdf6d87"><td class="mdescLeft">&#160;</td><td class="mdescRight">The alphabet to use; either the DNA nucleotides or amino acids.  <a href="class_argument_handler.html#ac2a6552abc7c6449b625791aefdf6d87">More...</a><br /></td></tr>
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<tr class="memitem:ae67a9e8d392b5fcc6f75c8fb7a875afd"><td class="memItemLeft" align="right" valign="top">enum &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="class_argument_handler.html#ae67a9e8d392b5fcc6f75c8fb7a875afd">CorrectionType</a> { <br />
&#160;&#160;<a class="el" href="class_argument_handler.html#ae67a9e8d392b5fcc6f75c8fb7a875afda3bc78094126089bb7a17ff4a5ef7e60f">not_assigned</a>, 
<a class="el" href="class_argument_handler.html#ae67a9e8d392b5fcc6f75c8fb7a875afda2c1d7a65ead4fefe3d70bfc2f64662e0">none</a>, 
<a class="el" href="class_argument_handler.html#ae67a9e8d392b5fcc6f75c8fb7a875afda73811e507c334774db6b1ab687639b5f">JukesCantor</a>, 
<a class="el" href="class_argument_handler.html#ae67a9e8d392b5fcc6f75c8fb7a875afda543fa5f6ad05da7f2efa6cefee5ba8d9">Kimura2</a>, 
<br />
&#160;&#160;<a class="el" href="class_argument_handler.html#ae67a9e8d392b5fcc6f75c8fb7a875afdab094fe12b9abab259fbf519b9e3399a3">FastTree</a>
<br />
 }</td></tr>
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<tr class="memitem:ad6143cf6a96ca5cc6aeb97f432bc629d"><td class="memItemLeft" align="right" valign="top">bool&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="class_argument_handler.html#ad6143cf6a96ca5cc6aeb97f432bc629d">getAbort</a> () const</td></tr>
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<tr class="memitem:ac6b6ce1eb3d6fee43314823c8c3e9e6c"><td class="memItemLeft" align="right" valign="top">std::string&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="class_argument_handler.html#ac6b6ce1eb3d6fee43314823c8c3e9e6c">getMethod</a> () const</td></tr>
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<tr class="memitem:a242123ae240bca20b782c544416e2fc3"><td class="memItemLeft" align="right" valign="top">std::string&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="class_argument_handler.html#a242123ae240bca20b782c544416e2fc3">getNJTmpDir</a> () const</td></tr>
<tr class="memdesc:a242123ae240bca20b782c544416e2fc3"><td class="mdescLeft">&#160;</td><td class="mdescRight">Get the temporary directory used for the neighbor-joining algorithm.  <a href="class_argument_handler.html#a242123ae240bca20b782c544416e2fc3">More...</a><br /></td></tr>
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<tr class="memitem:a32c069acf9792739ceb10c87edf22ddc"><td class="memItemLeft" align="right" valign="top"><a class="el" href="class_argument_handler.html#ae693a55bec1ed6005f0976a40a7f854a">InputType</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="class_argument_handler.html#a32c069acf9792739ceb10c87edf22ddc">getInputType</a> () const</td></tr>
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<tr class="memitem:a1c8fbd4a0c2b3d4235c3ef8b83fd43b8"><td class="memItemLeft" align="right" valign="top">FILE *&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="class_argument_handler.html#a1c8fbd4a0c2b3d4235c3ef8b83fd43b8">getOutputFile</a> () const</td></tr>
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<tr class="memitem:a56ce7d11969a9efb741fa10fc14deed2"><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="class_argument_handler.html#a56ce7d11969a9efb741fa10fc14deed2">getNumThreads</a> () const</td></tr>
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<tr class="memitem:a8b8d3d08a48c31c010aa80095f85e7cf"><td class="memItemLeft" align="right" valign="top"><a class="el" href="class_argument_handler.html#ac2a6552abc7c6449b625791aefdf6d87">AlphabetType</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="class_argument_handler.html#a8b8d3d08a48c31c010aa80095f85e7cf">getAlphabetType</a> () const</td></tr>
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<tr class="memitem:ad2b8028126c07aabb8603c44594ffaa6"><td class="memItemLeft" align="right" valign="top"><a class="el" href="class_argument_handler.html#ae67a9e8d392b5fcc6f75c8fb7a875afd">CorrectionType</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="class_argument_handler.html#ad2b8028126c07aabb8603c44594ffaa6">getCorrectionType</a> () const</td></tr>
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<tr class="memitem:a817493c9c676890ac210e1384191828c"><td class="memItemLeft" align="right" valign="top">bool&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="class_argument_handler.html#a817493c9c676890ac210e1384191828c">getUseSSE</a> () const</td></tr>
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Static Public Member Functions</h2></td></tr>
<tr class="memitem:aed3ea207ece08d71c49613911ac8b711"><td class="memItemLeft" align="right" valign="top">static bool&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="class_argument_handler.html#aed3ea207ece08d71c49613911ac8b711">argumentTest</a> ()</td></tr>
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<h2 class="groupheader">Member Enumeration Documentation</h2>
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<h2 class="memtitle"><span class="permalink"><a href="#ac2a6552abc7c6449b625791aefdf6d87">&#9670;&nbsp;</a></span>AlphabetType</h2>

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          <td class="memname">enum <a class="el" href="class_argument_handler.html#ac2a6552abc7c6449b625791aefdf6d87">ArgumentHandler::AlphabetType</a></td>
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<p>The alphabet to use; either the DNA nucleotides or amino acids. </p>
<table class="fieldtable">
<tr><th colspan="2">Enumerator</th></tr><tr><td class="fieldname"><a id="ac2a6552abc7c6449b625791aefdf6d87af8d1253b6d8eecce0eea5eff86ddc63e"></a>dna&#160;</td><td class="fielddoc"></td></tr>
<tr><td class="fieldname"><a id="ac2a6552abc7c6449b625791aefdf6d87abf0a7e58c2a951cb200e05ceed789d48"></a>amino&#160;</td><td class="fielddoc"></td></tr>
<tr><td class="fieldname"><a id="ac2a6552abc7c6449b625791aefdf6d87a340fde3e9bbd6b4f6450c7e10baa63a4"></a>null&#160;</td><td class="fielddoc"></td></tr>
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<a id="ae67a9e8d392b5fcc6f75c8fb7a875afd"></a>
<h2 class="memtitle"><span class="permalink"><a href="#ae67a9e8d392b5fcc6f75c8fb7a875afd">&#9670;&nbsp;</a></span>CorrectionType</h2>

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          <td class="memname">enum <a class="el" href="class_argument_handler.html#ae67a9e8d392b5fcc6f75c8fb7a875afd">ArgumentHandler::CorrectionType</a></td>
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<p>The correction algorithm to employ. The JukesCantor and Kimura2 methods are appropriate for DNA while FastTree is for amino acid alphabets. </p>
<table class="fieldtable">
<tr><th colspan="2">Enumerator</th></tr><tr><td class="fieldname"><a id="ae67a9e8d392b5fcc6f75c8fb7a875afda3bc78094126089bb7a17ff4a5ef7e60f"></a>not_assigned&#160;</td><td class="fielddoc"></td></tr>
<tr><td class="fieldname"><a id="ae67a9e8d392b5fcc6f75c8fb7a875afda2c1d7a65ead4fefe3d70bfc2f64662e0"></a>none&#160;</td><td class="fielddoc"></td></tr>
<tr><td class="fieldname"><a id="ae67a9e8d392b5fcc6f75c8fb7a875afda73811e507c334774db6b1ab687639b5f"></a>JukesCantor&#160;</td><td class="fielddoc"></td></tr>
<tr><td class="fieldname"><a id="ae67a9e8d392b5fcc6f75c8fb7a875afda543fa5f6ad05da7f2efa6cefee5ba8d9"></a>Kimura2&#160;</td><td class="fielddoc"></td></tr>
<tr><td class="fieldname"><a id="ae67a9e8d392b5fcc6f75c8fb7a875afdab094fe12b9abab259fbf519b9e3399a3"></a>FastTree&#160;</td><td class="fielddoc"></td></tr>
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<h2 class="memtitle"><span class="permalink"><a href="#ae693a55bec1ed6005f0976a40a7f854a">&#9670;&nbsp;</a></span>InputType</h2>

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<p>The input type can be either a set of alignments in FASTA format, or a pre-computed distance matrix in Phylip format. </p>
<table class="fieldtable">
<tr><th colspan="2">Enumerator</th></tr><tr><td class="fieldname"><a id="ae693a55bec1ed6005f0976a40a7f854aafe3d262ec86ee31ed3d27ef42b1f235a"></a>alignment&#160;</td><td class="fielddoc"></td></tr>
<tr><td class="fieldname"><a id="ae693a55bec1ed6005f0976a40a7f854aa9d20bc1085ccd1932c0ffd1d97a10dc6"></a>distance&#160;</td><td class="fielddoc"></td></tr>
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<h2 class="memtitle"><span class="permalink"><a href="#ae260b096d1b4cb57e0539b8d37ca1ce6">&#9670;&nbsp;</a></span>OutputType</h2>

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<p>The output type can be either a distance matrix or a tree. </p>
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<tr><th colspan="2">Enumerator</th></tr><tr><td class="fieldname"><a id="ae260b096d1b4cb57e0539b8d37ca1ce6a1af730d3ffbdc6354d6bda2549356cef"></a>dist&#160;</td><td class="fielddoc"></td></tr>
<tr><td class="fieldname"><a id="ae260b096d1b4cb57e0539b8d37ca1ce6ab25e481414af792cbeffe6f6e2f06301"></a>tree&#160;</td><td class="fielddoc"></td></tr>
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<h2 class="memtitle"><span class="permalink"><a href="#a2657983b12529181db92512d3a6fc1fa">&#9670;&nbsp;</a></span>ArgumentHandler()</h2>

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          <td class="paramtype">int&#160;</td>
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<h2 class="memtitle"><span class="permalink"><a href="#aed3ea207ece08d71c49613911ac8b711">&#9670;&nbsp;</a></span>argumentTest()</h2>

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<h2 class="memtitle"><span class="permalink"><a href="#ad6143cf6a96ca5cc6aeb97f432bc629d">&#9670;&nbsp;</a></span>getAbort()</h2>

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<h2 class="memtitle"><span class="permalink"><a href="#a8b8d3d08a48c31c010aa80095f85e7cf">&#9670;&nbsp;</a></span>getAlphabetType()</h2>

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<h2 class="memtitle"><span class="permalink"><a href="#ad2b8028126c07aabb8603c44594ffaa6">&#9670;&nbsp;</a></span>getCorrectionType()</h2>

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<h2 class="memtitle"><span class="permalink"><a href="#ad651123ca891c60ec98111817e38b06a">&#9670;&nbsp;</a></span>getInputFile()</h2>

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<h2 class="memtitle"><span class="permalink"><a href="#a32c069acf9792739ceb10c87edf22ddc">&#9670;&nbsp;</a></span>getInputType()</h2>

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<h2 class="memtitle"><span class="permalink"><a href="#ac6b6ce1eb3d6fee43314823c8c3e9e6c">&#9670;&nbsp;</a></span>getMethod()</h2>

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<h2 class="memtitle"><span class="permalink"><a href="#a242123ae240bca20b782c544416e2fc3">&#9670;&nbsp;</a></span>getNJTmpDir()</h2>

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<p>Get the temporary directory used for the neighbor-joining algorithm. </p>

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<h2 class="memtitle"><span class="permalink"><a href="#a56ce7d11969a9efb741fa10fc14deed2">&#9670;&nbsp;</a></span>getNumThreads()</h2>

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<h2 class="memtitle"><span class="permalink"><a href="#a1c8fbd4a0c2b3d4235c3ef8b83fd43b8">&#9670;&nbsp;</a></span>getOutputFile()</h2>

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<h2 class="memtitle"><span class="permalink"><a href="#ab0837386ce1c1f76280c9917572989dc">&#9670;&nbsp;</a></span>getOutputType()</h2>

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<h2 class="memtitle"><span class="permalink"><a href="#a817493c9c676890ac210e1384191828c">&#9670;&nbsp;</a></span>getUseSSE()</h2>

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<hr/>The documentation for this class was generated from the following files:<ul>
<li>NINJA/<a class="el" href="_argument_handler_8hpp_source.html">ArgumentHandler.hpp</a></li>
<li>NINJA/<a class="el" href="_argument_handler_8cpp.html">ArgumentHandler.cpp</a></li>
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